[BioC] Retrieving Upstream Sequences With biomaRt
Stephen Henderson
s.henderson at ucl.ac.uk
Tue Feb 20 13:11:02 CET 2007
The first code that you show doesn't work--for many reasons.
>library(biomaRt)
>ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl", mysql=TRUE)
>entrez <- c("100","330")
>gene <- getGene(id=entrez, type="entrezgene", mart=ens)
>getSequence(chromosome = gene$chromosome, start = gene$start - 2000,
end= >gene$end + 1000, mart=ens)
1. gene$start and gene$end don't exist.
2. seqType is not specified.
3. seqType can't be specified as the type you want.
>However, when I try the following line:
>gene <- getGene(id=entrez, type="entrezgene", mart=ens)
that appears to be a problem with your database installation as if you
do it over the web (i.e. drop mysql=TRUE):
ens<-useMart("ensembl",dataset="hsapiens_gene_ensembl")
entrez <- c("100","330")
gene <- getGene(id=entrez, type="entrezgene", mart=ens)
it works fine.
>The examples in the vignette all seem to work. What is wrong here?
Where is >the file mentioned in the error message supposed to live?
Stephen Henderson
Wolfson Inst. for Biomedical Research
Cruciform Bldg., Gower Street
University College London
United Kingdom, WC1E 6BT
+44 (0)207 679 6827
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